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==Overview==
While most microorganisms cannot survive in beer due to the hops, low pH, alcohol content, relatively high carbon dioxide, and shortage of nutrients, certain species are considered to be beer spoilage organisms due to their ability to adapt to brewing conditions (namely hops) and to form biofilms and survive in beer and make a potential impact on the beer's flavor by producing acidity, phenols, turbidity, and/or super-attenuation (which can cause gushing or in extreme cases exploding bottles/cans) with just a few surviving cells. Adaption Bacteria species that have adapted to the brewing environment also makes tend to be hop tolerant, but strains of the same species found outside of breweries are not tolerant of brewing conditions. It is thought that these species evolved to carry the genes to adapt to brewing conditions during the 5th to 9th centuries when hops were first being used in brewing, and that this evolution gave them more able a specialized adaption to survive the harsh brewing environment where few competitors can survive <ref name="Suzuki_2012">[https://onlinelibrary.wiley.com/doi/abs/10.1002/j.2050-0416.2011.tb00454.x 125th Anniversary Review: Microbiological Instability of beerBeer Caused by Spoilage Bacteria. Ken Suzuki. 2012. DOI: https://doi.org/10.1002/j.2050-0416.2011.tb00454.x]</ref>. These species Species of yeast and bacteria that are considered beer spoilers include [[Brettanomyces|''Brettanomyces'']] species, numerous [[Lactobacillus|''Lactobacillus'']] species, ''Pediococcus damnosus'', ''Pectinatus cerevisiphilus'' (anaerobe responsible for 20-30% of bacterial contaminations that produces acetic acid, propionic acid, acetoin, and 'rotten egg' like odors in contaminated beer), ''Pectinatus frisingensis'', ''Megasphaera cerevisiae'' (7% of bacterial contaminations; inhibited below pH 4.1 and 2.8% ABV but can produce considerable amounts of [[Butyric Acid|butyric acid]] along with smaller amounts of acetic acid, caproic acid, [[Isovaleric Acid|isovaleric acid]], acetoin, and hydrogen sulphide), ''Selenomonas lactifex'', ''Zymophilus'' spp., [[Saccharomyces#Saccharomyces_cerevisiae_var._diastaticus|''Saccharomyces cerevisiae'' var. ''diastaticus'']], and some species from the ''Candida'' and ''Pichia'' genera. Hop tolerant lactic acid bacteria make up the majority of contamination issues in breweries, with ''L. brevis'' making up more than half of the reported contaminations, and all lactic acid bacteria making up 60-90% of reported contaminations. A new species of ''Lactobacillus'' was recently identified called ''L. acetotolerans'' and was [https://www.facebook.com/groups/MilkTheFunk/permalink/1363048380390039/ responsible for contaminating Goose Island's Bourbon County Stout], which is 60 IBU and 11% ABV. In sour beers with a pH below 4.3, only some lactic acid bacteria, ''Brettanomyces'', and some wild ''Saccharomyces'' have the potential for unwanted growth, while beers with low alcohol, a small amount of hops, lower CO<sup>2</sup> volumes (cask ales and beers dispensed with nitrogen, for example), and higher pH (4.4-4.6) are the most susceptible to contamination. ''Zymomonas mobilis'' is a microaerophilic Gram-negative acetic acid bacteria that can withstand hops and can grow in bottled beer or casks where priming sugar is added and small amounts of air is present and produces high levels of acetaldehyde and hydrogen sulphide <ref name="Vaughan_2005">[https://onlinelibrary.wiley.com/doi/full/10.1002/j.2050-0416.2005.tb00221.x Enhancing the Microbiological Stability of Malt and Beer — A Review. Anne Vaughan, Tadhg O'Sullivan, Douwe Van Sinderen. 2005. DOI: https://doi.org/10.1002/j.2050-0416.2005.tb00221.x.]</ref>.
Other species of microbes do not grow in beer but can become contaminants earlier on in the brewing process (for example during kettle souring). These species include enterobacteria such as ''Clostridium'' species, ''Obesumbacterium proteus'' and ''Rahnella aquatilis'', and wild ''Saccharomyces'' that might not be able to grow in finished beer. Other species are considered "indicator" species because they do not directly cause spoilage of beer, but indicate that there is a hygiene problem. These include ''Acetobacter'', ''Gluconobacter'', and ''Klebsiella'' species, as well as aerobic yeasts, all of which usually don't have an impact when present unless oxygen is also present. They can also produce slime that protects other microorganisms that can have a greater impact on the beer's stability <ref name="Wirtanen_2001">[https://www.researchgate.net/publication/273439407_Disinfectant_testing_against_brewery-related_biofilms. Disinfectant testing against brewery-related biofilms. Erna Storgårds, Gun Wirtanen. 2001.]</ref><ref name="Bokulich_2018">[https://www.tandfonline.com/doi/abs/10.1094/ASBCJ-2012-0709-01 A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. Nicholas A. Bokulich, Charles W. Bamforth & David A. Mills. 2018.]</ref>. Some species can contaminate yeast pitches. ''Pediococcus damnosus'' is frequently the cause of such contaminations and can cause diacetyl problems, as well as ''Pediococcus inopinatus'', ''Pediocococcus claussenii'', ''L. casei'', ''Selenomonas lacticifex'', and ''Zymophilus raffinosivorans'' (although these are rarer to find in finished beer). ''Obesumbacterium proteus'' (which gives a parsnip-like smell and flavor) and ''Rahnella aquatilis'' can contaminate yeast pitches, and can inhibit fermentation and result in the beer finishing at a higher pH <ref name="Vaughan_2005" />.
Bokulich et al. (2015) studied the microbial populations throughout a brewery (presumably Allagash) that produces clean beer, mixed fermentation sour beer, and spontaneously fermented coolship ale. They found that most of the microbes living in breweries were introduced from the ingredients such as malted barley and hops, and many populations were confined to specific rooms or areas within the brewery. Some species did spread to other rooms, presumably through human and insect vectors. Beer resistant lactic acid bacteria spread throughout the brewery (although more abundantly found near packaging equipment and fermenters that were filled with sour beer), but the clean beer was largely uncontaminated. Physical partitions and walls appeared to help inhibit the spread of microbes from room to room <ref name="Bokulich_2015">[https://elifesciences.org/articles/04634 Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance. Nicholas A Bokulich, Jordyn Bergsveinson, Barry Ziola, David A Mills. 2015.]</ref>.
Ale yeast was found throughout the brewery, especially in the fermentation cellar. Malted grains were determined to be the highest source of potentially contaminating microbes (mostly ''Pediococcus'', although the PCR method used in the study was not adequate for detecting microbes on grain) in the hotside areas of the brewery compared to other microbe sources such as human skin, outdoor air, soil, saliva, feces, water from the plumbing, etc. Hops were determined to be the highest source of microbes in the cellar fermentation areas (''Pediococcus'' spp, ''Lactobacillus lindneri'', and ''L. brevis'' were detected on pellet hops, although the presence of hop tolerant genes was not detected from microbes found on hops), and yeast was the highest population in fermenter and packaging areas. While human skin was a minor contributor to microbe populations found in the brewery, oak barrel surfaces were populated with microbes from unknown sources. Therefore, it was determined in this study that raw materials are the major source for potential contaminants in a brewery, although minor sources such as sinks are still potential problems and hop tolerant species were linked to the purposeful inoculation of souring microbes in the sour beer production itself <ref name="Bokulich_2015" />. ''L. lindneri'' is highly hop tolerant, difficult to detect on MRS media, and has been found to survive suboptimal heat pasteurization temperatures. ''L. brevis'' strains that have been growing in beer are also hop tolerant, although some strains have been found to lose their ability to grow in beer if they are grown in lab media after a few generations and strains not found in breweries are not hop tolerant, which suggests that strains found in beer have adapted to that environment. Both of these species also have a smaller cell size when they have been growing in beer, and can pass through microbial filtration systems <ref name="Suzuki_2012">[https://onlinelibrary.wiley.com/doi/abs/10.1002/j.2050-0416.2011.tb00454.x 125th Anniversary Review: Microbiological Instability of Beer Caused by Spoilage Bacteria. Ken Suzuki. 2012. DOI: https://doi.org/10.1002/j.2050-0416.2011.tb00454.x]</ref>.
Seasonality played a minor role in the populations of microbes throughout the brewery, with ale yeast and ''Candida santamariae'' spreading from the fermentation and packaging area to the rest of the brewery from fall to summer (it was proposed that the warming from fall to summer played a role in the spread of ale yeast and ''Candida santamariae'' throughout the brewery). ''Micrococcus'' and ''Kocuria'' were found in more localized areas such as the floors and other surfaces in the barrel room, cellar, and packaging room. ''Acetobacter'' and ''Lactobacillus'' were found specifically in areas where a lot of wort or beer was being processed (conveyor belts and floors below the packaging equipment, hotside and cellar area sinks, and sample ports on kegs and fermenters). ''Lactobacillus'' was more common on surfaces where sour beer production was (fermenters and barrel surfaces), with floor surfaces having a more diverse mixture of LAB species <ref name="Bokulich_2015" />.